Locus 5833

Sequence ID 3L_DroMel_CAF1
Location 15,755,834 – 15,756,102
Length 268
Max. P 0.897396
window9284 window9285 window9286 window9287 window9288 window9289 window9290

overview

Window 4

Location 15,755,834 – 15,755,946
Length 112
Sequences 4
Columns 112
Reading direction forward
Mean pairwise identity 85.59
Mean single sequence MFE -28.23
Consensus MFE -21.02
Energy contribution -21.96
Covariance contribution 0.94
Combinations/Pair 1.18
Mean z-score -1.71
Structure conservation index 0.74
SVM decision value 0.39
SVM RNA-class probability 0.716235
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15755834 112 + 23771897
AAUGUCGAAAGCAAUUUCCUGGAUGGGUUCGUAGAGGAAAAUUGCCGGCGGAACAAGGCAAUUCAAGAUUCAAAACAUAUAGAAUUGGGCUAAUGCCUUUGGAUUUUUAGAU
..(((((...((((((((((..(((....)))..))).))))))))))))..............((((((((((.((........))(((....)))))))))))))..... ( -25.80)
>DroSec_CAF1 7477 110 + 1
AAUGUCGAAAGCAAUUUCCUGGAUGGGUUCAUAGAGGAAAAUUGCCGGCGGAACAAGGCAAUUGAAGAUUCAAAG--UAUAGAACUGGGCUAAUGCCCUUAGAUUUUUAGAU
..(((((...((((((((((..(((....)))..))).))))))))))))...........((((((((..((((--(.....)))((((....))))))..)))))))).. ( -27.60)
>DroSim_CAF1 7742 102 + 1
AAUGUCGAAAGCAAUUUCCUGGA--------UAGAGGAAAAUUGCCGGCGGAACAAGGCAAUUGAAGAUUCAAAG--UAUAGAACUGGGCUAAUGCCUCUGAAUUUUCAGAU
..(((((...((((((((((...--------...))).))))))))))))...........(((((((((((.((--(.....)))((((....)))).))))))))))).. ( -29.30)
>DroEre_CAF1 7580 110 + 1
AAUGUCGAAAGCAAUUUCCUGGACGGGUUCAUGGGGGCAAAUUGCAGUCGGAACAAGGCAAUUGAAGAUUCAAAG--UGCAGGACUGGGACAAUGCUUUCAGAUUUUCAGAU
...((((((((((.(.(((..(.(..((((.(((..((.....))..)))))))..)(((.((((....))))..--)))....)..))).).))))))).)))........ ( -30.20)
>consensus
AAUGUCGAAAGCAAUUUCCUGGAUGGGUUCAUAGAGGAAAAUUGCCGGCGGAACAAGGCAAUUGAAGAUUCAAAG__UAUAGAACUGGGCUAAUGCCUUUAGAUUUUCAGAU
..((((....((((((((((..(((....)))..))).))))))).(......)..)))).((((((((((((.............((((....)))))))))))))))).. (-21.02 = -21.96 +   0.94)

alignment

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secondary structure

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Window 5

Location 15,755,834 – 15,755,946
Length 112
Sequences 4
Columns 112
Reading direction reverse
Mean pairwise identity 85.59
Mean single sequence MFE -21.36
Consensus MFE -15.59
Energy contribution -16.34
Covariance contribution 0.75
Combinations/Pair 1.15
Mean z-score -1.48
Structure conservation index 0.73
SVM decision value 0.06
SVM RNA-class probability 0.562387
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15755834 112 - 23771897
AUCUAAAAAUCCAAAGGCAUUAGCCCAAUUCUAUAUGUUUUGAAUCUUGAAUUGCCUUGUUCCGCCGGCAAUUUUCCUCUACGAACCCAUCCAGGAAAUUGCUUUCGACAUU
.............((((((........((((..........)))).......))))))....((..((((((((.(((..............)))))))))))..))..... ( -18.60)
>DroSec_CAF1 7477 110 - 1
AUCUAAAAAUCUAAGGGCAUUAGCCCAGUUCUAUA--CUUUGAAUCUUCAAUUGCCUUGUUCCGCCGGCAAUUUUCCUCUAUGAACCCAUCCAGGAAAUUGCUUUCGACAUU
.............((((((........((((....--....)))).......))))))....((..((((((((.(((..(((....)))..)))))))))))..))..... ( -22.86)
>DroSim_CAF1 7742 102 - 1
AUCUGAAAAUUCAGAGGCAUUAGCCCAGUUCUAUA--CUUUGAAUCUUCAAUUGCCUUGUUCCGCCGGCAAUUUUCCUCUA--------UCCAGGAAAUUGCUUUCGACAUU
.(((((....)))))((((........((((....--....)))).......))))......((..((((((((.(((...--------...)))))))))))..))..... ( -23.46)
>DroEre_CAF1 7580 110 - 1
AUCUGAAAAUCUGAAAGCAUUGUCCCAGUCCUGCA--CUUUGAAUCUUCAAUUGCCUUGUUCCGACUGCAAUUUGCCCCCAUGAACCCGUCCAGGAAAUUGCUUUCGACAUU
...........((((((((...(((.......(((--..((((....)))).)))...((((.....((.....))......)))).......)))...))))))))..... ( -20.50)
>consensus
AUCUAAAAAUCCAAAGGCAUUAGCCCAGUUCUAUA__CUUUGAAUCUUCAAUUGCCUUGUUCCGCCGGCAAUUUUCCUCUAUGAACCCAUCCAGGAAAUUGCUUUCGACAUU
.............((((((........((((..........)))).......))))))....((..((((((((.(((..(((....)))..)))))))))))..))..... (-15.59 = -16.34 +   0.75)

alignment

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secondary structure

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Window 6

Location 15,755,871 – 15,755,986
Length 115
Sequences 4
Columns 115
Reading direction forward
Mean pairwise identity 88.45
Mean single sequence MFE -28.10
Consensus MFE -21.61
Energy contribution -22.73
Covariance contribution 1.12
Combinations/Pair 1.17
Mean z-score -1.56
Structure conservation index 0.77
SVM decision value 0.19
SVM RNA-class probability 0.626662
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15755871 115 + 23771897
AAAAUUGCCGGCGGAACAAGGCAAUUCAAGAUUCAAAACAUAUAGAAUUGGGCUAAUGCCUUUGGAUUUUUAGAUGGCUGUUGUUAAGCCCAAUAAAAGCAAAAGCCAAUGCCGU
........(((((......(((.(((((((((((..........)))))((((....))))))))))(((((...((((.......))))...)))))......)))..))))). ( -27.60)
>DroSec_CAF1 7514 113 + 1
AAAAUUGCCGGCGGAACAAGGCAAUUGAAGAUUCAAAG--UAUAGAACUGGGCUAAUGCCCUUAGAUUUUUAGAUGGCUGUUGUUAAGCCCAAUAAAAGCAAAAGCCAAUGCCUU
.................((((((.((((((((..((((--(.....)))((((....))))))..)))))))).(((((.(((((............))))).))))).)))))) ( -28.70)
>DroSim_CAF1 7771 113 + 1
AAAAUUGCCGGCGGAACAAGGCAAUUGAAGAUUCAAAG--UAUAGAACUGGGCUAAUGCCUCUGAAUUUUCAGAUGACUGUUGUUAAGCCCAAUAAAAGCAAAAGCCAAUGCCAU
...((((..(((..(((((((((.(((((((((((.((--(.....)))((((....)))).))))))))))).)).)).)))))..)))))))....(((........)))... ( -29.60)
>DroEre_CAF1 7617 113 + 1
CAAAUUGCAGUCGGAACAAGGCAAUUGAAGAUUCAAAG--UGCAGGACUGGGACAAUGCUUUCAGAUUUUCAGAUGGCUGUUGUUAAGCCCAAUAAAGGCCAAAGCCAUUGCCGU
...........(((..((((((..(((((((((..(((--.(((............))))))..))))))))).(((((.(((((......))))).)))))..))).)))))). ( -26.50)
>consensus
AAAAUUGCCGGCGGAACAAGGCAAUUGAAGAUUCAAAG__UAUAGAACUGGGCUAAUGCCUUUAGAUUUUCAGAUGGCUGUUGUUAAGCCCAAUAAAAGCAAAAGCCAAUGCCGU
...................((((.((((((((((((.............((((....)))))))))))))))).(((((.(((((............))))).))))).)))).. (-21.61 = -22.73 +   1.12)

alignment

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secondary structure

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Window 7

Location 15,755,871 – 15,755,986
Length 115
Sequences 4
Columns 115
Reading direction reverse
Mean pairwise identity 88.45
Mean single sequence MFE -26.27
Consensus MFE -20.75
Energy contribution -20.50
Covariance contribution -0.25
Combinations/Pair 1.23
Mean z-score -1.40
Structure conservation index 0.79
SVM decision value -0.01
SVM RNA-class probability 0.528939
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15755871 115 - 23771897
ACGGCAUUGGCUUUUGCUUUUAUUGGGCUUAACAACAGCCAUCUAAAAAUCCAAAGGCAUUAGCCCAAUUCUAUAUGUUUUGAAUCUUGAAUUGCCUUGUUCCGCCGGCAAUUUU
.((((...((((..((((((((((.((((.......)))).......)))..)))))))..))))((((((.................)))))).........))))........ ( -27.53)
>DroSec_CAF1 7514 113 - 1
AAGGCAUUGGCUUUUGCUUUUAUUGGGCUUAACAACAGCCAUCUAAAAAUCUAAGGGCAUUAGCCCAGUUCUAUA--CUUUGAAUCUUCAAUUGCCUUGUUCCGCCGGCAAUUUU
((((((..((((..((((((((...((((.......))))...........))))))))..))))..((((....--....)))).......))))))................. ( -25.94)
>DroSim_CAF1 7771 113 - 1
AUGGCAUUGGCUUUUGCUUUUAUUGGGCUUAACAACAGUCAUCUGAAAAUUCAGAGGCAUUAGCCCAGUUCUAUA--CUUUGAAUCUUCAAUUGCCUUGUUCCGCCGGCAAUUUU
((((.(((((((..((((.......((((.......)))).(((((....)))))))))..)).))))).)))).--............(((((((..........))))))).. ( -27.30)
>DroEre_CAF1 7617 113 - 1
ACGGCAAUGGCUUUGGCCUUUAUUGGGCUUAACAACAGCCAUCUGAAAAUCUGAAAGCAUUGUCCCAGUCCUGCA--CUUUGAAUCUUCAAUUGCCUUGUUCCGACUGCAAUUUG
..(((((((.(((((((((.....)))))......(((....)))........))))))))))).(((((..(((--..((((....))))......)))...)))))....... ( -24.30)
>consensus
ACGGCAUUGGCUUUUGCUUUUAUUGGGCUUAACAACAGCCAUCUAAAAAUCCAAAGGCAUUAGCCCAGUUCUAUA__CUUUGAAUCUUCAAUUGCCUUGUUCCGCCGGCAAUUUU
..(((....(((((((.(((((...((((.......))))...)))))...)))))))....)))........................(((((((..........))))))).. (-20.75 = -20.50 +  -0.25)

alignment

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secondary structure

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Window 8

Location 15,755,946 – 15,756,062
Length 116
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 90.25
Mean single sequence MFE -29.62
Consensus MFE -25.98
Energy contribution -25.98
Covariance contribution -0.00
Combinations/Pair 1.15
Mean z-score -1.36
Structure conservation index 0.88
SVM decision value 0.05
SVM RNA-class probability 0.559791
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15755946 116 - 23771897
GA----AUAUUAGCCAUACUGAUUGUGAAAUUCUGCAAUUUGCCUGGCUAACUUGUGUGCCGAAAUGCUUUUGUUAAUUGACGGCAUUGGCUUUUGCUUUUAUUGGGCUUAACAACAGCC
..----...(((((((..(.((((((........)))))).)..))))))).((((..(((..((((((.(((.....))).))))))(((....))).......)))...))))..... ( -28.20)
>DroSec_CAF1 7587 120 - 1
GUACAUAUAUUAGCUAUACUGAUUGUGAAAUUCUGCAAUUUGCCUGGCCAACUUGUGUGCCGAAAUGCUUUUGUUAAUUGAAGGCAUUGGCUUUUGCUUUUAUUGGGCUUAACAACAGCC
(((((((..((.((((..(.((((((........)))))).)..)))).))..)))))))......(((.(((((((..((((((....))))))((((.....))))))))))).))). ( -31.60)
>DroSim_CAF1 7844 116 - 1
GA----AUAUUAGCCAUACUGAUUGUAAAAUUCUGCAAUUUGCCUGGCUAACUAGUGUGCCGAAAUGCUUUUGUUAAUUGAUGGCAUUGGCUUUUGCUUUUAUUGGGCUUAACAACAGUC
..----...(((((((..(.(((((((......))))))).)..)))))))((((((.((.((((.(((..(((((.....)))))..)))))))))...)))))).............. ( -28.50)
>DroEre_CAF1 7690 116 - 1
UA----AAAUUGGCCACAAUUAUUGUGAAAUUCUGCAGUUUGUCUGGCCAACUUGUGUGCCGAAAUGCUUUUGUUAAUUGACGGCAAUGGCUUUGGCCUUUAUUGGGCUUAACAACAGCC
..----...(((((((.....(((((........))))).....)))))))......(((((.(((((....))..)))..)))))..(((((((((((.....))))....))).)))) ( -30.20)
>consensus
GA____AUAUUAGCCAUACUGAUUGUGAAAUUCUGCAAUUUGCCUGGCCAACUUGUGUGCCGAAAUGCUUUUGUUAAUUGACGGCAUUGGCUUUUGCUUUUAUUGGGCUUAACAACAGCC
.........(((((((....(((((((......)))))))....))))))).((((..(((..((((((.(((.....))).))))))(((....))).......)))...))))..... (-25.98 = -25.98 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 15,755,986 – 15,756,102
Length 116
Sequences 3
Columns 116
Reading direction forward
Mean pairwise identity 71.39
Mean single sequence MFE -18.07
Consensus MFE -13.26
Energy contribution -13.27
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -1.14
Structure conservation index 0.73
SVM decision value 0.60
SVM RNA-class probability 0.796096
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15755986 116 + 23771897
CAAUUAACAAAAGCAUUUCGGCACACAAGUUAGCCAGGCAAAUUGCAGAAUUUCACAAUCAGUAUGGCUAAUAUUCCUUAAACAUUCUUUUGUGCGCCUUCUAUAAAUACUAGGUC
...................(((.(((((((((((((.((..((((..........))))..)).)))))))).................))))).))).................. ( -21.82)
>DroSim_CAF1 7884 89 + 1
CAAUUAACAAAAGCAUUUCGGCACACUAGUUAGCCAGGCAAAUUGCAGAAUUUUACAAUCAGUAUGGCUAAUAUUCCAUAAA---------------------------CUGGGUC
............((......))......((((((((.((..((((..........))))..)).))))))))..((((....---------------------------.)))).. ( -16.10)
>DroEre_CAF1 7730 100 + 1
CAAUUAACAAAAGCAUUUCGGCACACAAGUUGGCCAGACAAACUGCAGAAUUUCACAAUAAUUGUGGCCAAUUUUACCUAAAUAUCGCUAUGA----------------CCGAAAC
...............((((((.....(((((((((((.....)))........((((.....))))))))))))..........((.....))----------------)))))). ( -16.30)
>consensus
CAAUUAACAAAAGCAUUUCGGCACACAAGUUAGCCAGGCAAAUUGCAGAAUUUCACAAUCAGUAUGGCUAAUAUUCCAUAAA_AU___U_UG_________________CUGGGUC
............((......))......((((((((.((..((((..........))))..)).))))))))............................................ (-13.26 = -13.27 +   0.00)

alignment

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secondary structure

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Window 0

Location 15,755,986 – 15,756,102
Length 116
Sequences 3
Columns 116
Reading direction reverse
Mean pairwise identity 71.39
Mean single sequence MFE -25.67
Consensus MFE -15.12
Energy contribution -14.57
Covariance contribution -0.55
Combinations/Pair 1.17
Mean z-score -1.70
Structure conservation index 0.59
SVM decision value 1.00
SVM RNA-class probability 0.897396
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15755986 116 - 23771897
GACCUAGUAUUUAUAGAAGGCGCACAAAAGAAUGUUUAAGGAAUAUUAGCCAUACUGAUUGUGAAAUUCUGCAAUUUGCCUGGCUAACUUGUGUGCCGAAAUGCUUUUGUUAAUUG
(((..(((((((......(((((((((...(((((((...)))))))(((((..(.((((((........)))))).)..)))))...))))))))).)))))))...)))..... ( -33.00)
>DroSim_CAF1 7884 89 - 1
GACCCAG---------------------------UUUAUGGAAUAUUAGCCAUACUGAUUGUAAAAUUCUGCAAUUUGCCUGGCUAACUAGUGUGCCGAAAUGCUUUUGUUAAUUG
....(((---------------------------((.(..(((..(((((((..(.(((((((......))))))).)..)))))))...((((......)))))))..).))))) ( -19.50)
>DroEre_CAF1 7730 100 - 1
GUUUCGG----------------UCAUAGCGAUAUUUAGGUAAAAUUGGCCACAAUUAUUGUGAAAUUCUGCAGUUUGUCUGGCCAACUUGUGUGCCGAAAUGCUUUUGUUAAUUG
(((((((----------------((((((...(((....)))...(((((((.....(((((........))))).....))))))).))))).)))))))).............. ( -24.50)
>consensus
GACCCAG_________________CA_A___AU_UUUAAGGAAUAUUAGCCAUACUGAUUGUGAAAUUCUGCAAUUUGCCUGGCUAACUUGUGUGCCGAAAUGCUUUUGUUAAUUG
.............................................(((((((....(((((((......)))))))....)))))))...((((......))))............ (-15.12 = -14.57 +  -0.55)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:01:25 2006